2025
Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophsGuidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)
Loughran G, Andreev D, Terenin I, Namy O, Mikl M, Yordanova M, McManus C, Firth A, Atkins J, Fraser C, Ignatova Z, Iwasaki S, Kufel J, Larsson O, Leidel S, Mankin A, Mariotti M, Tanenbaum M, Topisirovic I, Vázquez-Laslop N, Viero G, Caliskan N, Chen Y, Clark P, Dinman J, Farabaugh P, Gilbert W, Ivanov P, Kieft J, Mühlemann O, Sachs M, Shatsky I, Sonenberg N, Steckelberg A, Willis A, Woodside M, Valasek L, Dmitriev S, Baranov P. Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nature Structural & Molecular Biology 2025, 32: 418-430. PMID: 40033152, DOI: 10.1038/s41594-025-01492-x.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteGene expression reportersStop codon readthroughRibosome entry siteEukaryotic translationTranscription initiationAntisense transcriptsRegulatory elementsRibosomal frameshiftingCodon readthroughExpression reportersEntry siteDual reportersUnconventional mechanismSequencePolyadenylationMisinterpretation of dataExpressionReadthroughFrameshiftSplicingTranscriptionEvaluate published dataMinimal requirementsProteinS-Nitrosylation of CRTC1 in Alzheimer’s disease impairs CREB-dependent gene expression induced by neuronal activity
Zhang X, Vlkolinsky R, Wu C, Dolatabadi N, Scott H, Prikhodko O, Zhang A, Blanco M, Lang N, Piña-Crespo J, Nakamura T, Roberto M, Lipton S. S-Nitrosylation of CRTC1 in Alzheimer’s disease impairs CREB-dependent gene expression induced by neuronal activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2418179122. PMID: 40014571, PMCID: PMC11892585, DOI: 10.1073/pnas.2418179122.Peer-Reviewed Original ResearchConceptsActivity-dependent gene expressionGene expressionAlzheimer's diseaseCREB-dependent gene expressionS-nitrosylationNitric oxide (NO)-related speciesTargets of S-nitrosylationNeuronal activity-dependent gene expressionPathogenesis of ADDecreased neurite lengthIncreased neuronal cell deathNeuronal cell deathSynaptic plasticityTranscriptional pathwaysCell deathCRISPR/Cas9 techniqueTranscription coactivator 1AD modelLong-term memory formationIncreased S-nitrosylationLong-term potentiationTherapeutic targetExpressionNeurite lengthCerebrocortical neuronsStructural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides
Hainzl T, Scortti M, Lindgren C, Grundström C, Krypotou E, Vázquez-Boland J, Sauer-Eriksson A. Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides. Cell Reports 2025, 44: 115290. PMID: 39970044, DOI: 10.1016/j.celrep.2025.115290.Peer-Reviewed Original ResearchConceptsDNA-binding helix-turn-helix motifInhibit virulence gene expressionVirulence gene expressionPathogen Listeria monocytogenesPrfA activityVirulence factorsPrfAMaster regulatorsHydrophobic residuesInhibitory bindingGene expressionStructural basisBinding promiscuityPeptide bindingBinding sitesConformational changesPeptide residuesOligopeptidesPeptideInhibitory peptidesBindingPeptide backboneResiduesPromiscuous inhibitionExpressionA comprehensive spatio-cellular map of the human hypothalamus
Tadross J, Steuernagel L, Dowsett G, Kentistou K, Lundh S, Porniece M, Klemm P, Rainbow K, Hvid H, Kania K, Polex-Wolf J, Knudsen L, Pyke C, Perry J, Lam B, Brüning J, Yeo G. A comprehensive spatio-cellular map of the human hypothalamus. Nature 2025, 639: 708-716. PMID: 39910307, PMCID: PMC11922758, DOI: 10.1038/s41586-024-08504-8.Peer-Reviewed Original ResearchConceptsGenome-wide association study genesRare deleterious variantsHypothalamic cell typesCell typesSingle-nucleus sequencingBody mass indexTranscription mapDeleterious variantsNeuronal cell typesG protein-coupled receptorsStudy genesBiological functions1Spatial transcriptomicsTranscriptomic identityCellular componentsExpression levelsPro-opiomelanocortin neuronsHuman hypothalamusAssociated with body mass indexPopulation levelMetabolic disordersHypothalamic cellsExpressionNeuronal clustersTranscriptomeResolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Pal A, Noble M, Morales M, Pal R, Baumgartner M, Yang J, Yim K, Uebbing S, Noonan J. Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment. Cell 2025, 188: 1504-1523.e27. PMID: 39889695, PMCID: PMC11928272, DOI: 10.1016/j.cell.2025.01.007.Peer-Reviewed Original Research
2024
RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs
Li Y, Liu X, Cheng F, Pan X, Yang Y. RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs. 2024, 00: 48-53. DOI: 10.1109/bibm62325.2024.10821865.Peer-Reviewed Original ResearchMultiple RNA-binding proteinsRNA-binding proteinsRNA transcriptsRNA-protein binding sitesRBP binding sitesFull-length transcriptsBinding sitesPredicted binding siteSequence dataRNA informationRNA fragmentsGene expressionTranscriptionRNASequence lengthSequenceSitesGenesProteinMachine learning methodsImbalanced labelsImbalanced dataData imbalanceFragmentsExpressionEvolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum
Marshall K, Stadtmauer D, Maziarz J, Wagner G, Lesch B. Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum. Developmental Cell 2024, 60: 646-664.e8. PMID: 39536760, PMCID: PMC11859772, DOI: 10.1016/j.devcel.2024.10.013.Peer-Reviewed Original ResearchPlacental mammalsLevel of transcriptionSingle-cell dataGene expression patternsMammalian spermatogenesisGene expression programsEpigenomic dataAdult testisEvolutionary innovationSpermatogenic cellsGene setsSpermatogenic developmentModel marsupialOpossum Monodelphis domesticaGene expressionExpression patternsGenesDevelopmental processesExpression programsSpermatogenesisMonodelphis domesticaMammalsDevelopmental timeCombination of featuresExpressionDetecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets
Zhou H, Lin W, Labra S, Lipton S, Elman J, Schork N, Rangan A. Detecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2024, 22: 27-38. PMID: 39471117, DOI: 10.1109/tcbb.2024.3487434.Peer-Reviewed Original ResearchSubsets of genesGene-gene relationshipsGene expression dataGene-gene interactionsGene expression datasetsRNA-sequencing data setsDetected biclustersExpression datasetsGene pathwaysSubsets of cellsGenesRegulatory effectsBiclusteringCorrelated expressionAsymmetric interactionsSymmetric interactionsInteractionExpressionCellsFunction and evolution of Ir52 receptors in mate detection in Drosophila
Luo Y, Talross G, Carlson J. Function and evolution of Ir52 receptors in mate detection in Drosophila. Current Biology 2024, 34: 5395-5408.e6. PMID: 39471807, PMCID: PMC11614688, DOI: 10.1016/j.cub.2024.10.001.Peer-Reviewed Original ResearchMating partnersCluster of genesPotential mating partnersSexually dimorphic neuronsCourtship behaviorEvolutionary timeMate detectionExpression systemFly legFruit flyFly speciesSpeciesBiological problemsTaste neuronsMatingPheromone extractsFliesReceptorsDrosophilaCourtshipGenesNeuronsPheromoneCircuit mappingExpressionMachine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cellsPhysalia gonodendra are not yet sexually mature when released
Oguchi K, Yamamoto G, Kohtsuka H, Dunn C. Physalia gonodendra are not yet sexually mature when released. Scientific Reports 2024, 14: 23011. PMID: 39362967, PMCID: PMC11450099, DOI: 10.1038/s41598-024-73611-5.Peer-Reviewed Original ResearchConceptsGerm cell maturationGene expression analysisGerm cell markersReproductive ecologySexual reproductionHaploid cellsGerm cellsReproductive biologyGonophoresExpression analysisRelated genesLife cycleGenesCell maturationGermConsistent with other studiesFlow cytometryPhysalia utriculusExpressionCnidariaCell markersCellsPhysaliaSpermHydrozoaPIWI-interacting RNAs: who, what, when, where, why, and how
Haase A, Ketting R, Lai E, van Rij R, Siomi M, Svoboda P, van Wolfswinkel J, Wu P. PIWI-interacting RNAs: who, what, when, where, why, and how. The EMBO Journal 2024, 43: 5335-5339. PMID: 39327528, PMCID: PMC11574264, DOI: 10.1038/s44318-024-00253-8.Peer-Reviewed Original ResearchPIWI-interacting RNAsPiRNA biologySelfish genetic elementsAdult mammalian testisGerm cell biologyRegulate gene expressionPIWI proteinsMammalian testisGenetic elementsEvolutionary biologistsAntiviral defenseGene expressionCell biologyBiologyPIWIRNATestisGeneticistsBiologistsProteinGermPlanariaDefenseExpressionBiochemistsEORTC stomach cancer PD-L1 biomarker European initiative: the ASPIRE study protocol
Petrillo A, Oudijk L, Sundar R, Daumer C, Casas J, D’Haese D, Mauer M, van Grieken N, Smyth E, Moehler M. EORTC stomach cancer PD-L1 biomarker European initiative: the ASPIRE study protocol. ESMO Gastrointestinal Oncology 2024, 5: 100071. DOI: 10.1016/j.esmogo.2024.100071.Peer-Reviewed Original ResearchPredicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs
Song T, Cosatto E, Wang G, Kuang R, Gerstein M, Min M, Warrell J. Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. Bioinformatics 2024, 40: ii111-ii119. PMID: 39230702, PMCID: PMC11373608, DOI: 10.1093/bioinformatics/btae383.Peer-Reviewed Original ResearchConceptsGene expressionSpatial gene expressionSpatial transcriptomics technologiesTissue histology imagesExpressed genesGene activationTranscriptomic technologiesMolecular underpinningsGraph neural networksState-of-the-artSpatial expressionGenesTissue architectureExpressionHistological imagesNeural networkLeveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach
Frank M, Ni P, Jensen M, Gerstein M. Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2320510121. PMID: 39110734, PMCID: PMC11331094, DOI: 10.1073/pnas.2320510121.Peer-Reviewed Original ResearchConceptsProtein phase transitionsAssociated with reduced gene expressionProtein structure predictionAlzheimer's disease-related proteinsDisease-related proteinsAlzheimer's diseaseProtein sequencesSequence variantsStructure predictionAmyloid aggregatesProtein designGene expressionAge-related diseasesNatural defense mechanismsSoluble stateProteinDefense mechanismsBiophysical featuresAlzheimerSequenceAmyloidVariantsExpressionLanguage modelComputational frameworkGP100 expression is variable in intensity in melanoma
Mann J, Hasson N, Su D, Adeniran A, Smalley K, Djureinovic D, Jilaveanu L, Schoenfeld D, Kluger H. GP100 expression is variable in intensity in melanoma. Cancer Immunology, Immunotherapy 2024, 73: 191. PMID: 39105816, PMCID: PMC11303354, DOI: 10.1007/s00262-024-03776-5.Peer-Reviewed Original ResearchConceptsGp100 expressionCutaneous melanomaTreatment of cutaneous melanomaAdvanced cutaneous melanomaT-cell engagersImprove patient selectionMetastatic melanomaUveal melanomaMetastatic samplesPatient selectionClinical trialsMelanomaQuantitative immunofluorescence methodGp100Improve outcomesImmunofluorescence methodTherapeutic intentDrugCellular productsExpressionTebentafuspImmunohistochemistryCancer cell – Fibroblast crosstalk via HB-EGF, EGFR, and MAPK signaling promotes the expression of macrophage chemo-attractants in squamous cell carcinoma
Giangreco G, Rullan A, Naito Y, Biswas D, Liu Y, Hooper S, Nenclares P, Bhide S, Chon U Cheang M, Chakravarty P, Hirata E, Swanton C, Melcher A, Harrington K, Sahai E. Cancer cell – Fibroblast crosstalk via HB-EGF, EGFR, and MAPK signaling promotes the expression of macrophage chemo-attractants in squamous cell carcinoma. IScience 2024, 27: 110635. PMID: 39262776, PMCID: PMC11387794, DOI: 10.1016/j.isci.2024.110635.Peer-Reviewed Original ResearchTumor microenvironmentSquamous cell carcinoma cohortCancer cellsMacrophage chemo-attractantsSquamous cell carcinomaTumor-stroma crosstalkRecruitment of macrophagesExpression of CSF2Prognostic significanceCarcinoma cohortCell carcinomaPatient prognosisHB-EGFStromal fibroblastsCancer outcomesCancer progressionCancerMAPK signalingIndicator of signalingChemo-attractantsCellsFibroblastsCarcinomaExpressionEGFRRepresenting core gene expression activity relationships using the latent structure implicit in Bayesian networks
Gao J, Gerstein M. Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinformatics 2024, 40: btae463. PMID: 39051682, PMCID: PMC11316617, DOI: 10.1093/bioinformatics/btae463.Peer-Reviewed Original ResearchTranscriptional regulatory networksGene regulatory networksCo-expression networkGene expression activityChIP-seqGene conservationCluster genesSupplementary dataRegulatory networksBiological networksClearer clusteringCo-expressionExpression activityBioinformaticsGenesBiomedical studiesConservationExpressionClustersDNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism
Xiao C, Peng G, Conneely K, Zhao H, Felger J, Wommack E, Higgins K, Shin D, Saba N, Bruner D, Miller A. DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism. Molecular Psychiatry 2024, 30: 76-83. PMID: 38977918, DOI: 10.1038/s41380-024-02652-z.Peer-Reviewed Original ResearchGene expressionMethylation lociAssociated with gene expressionHead and neck cancerDNA methylation profilesProtein markersLipid metabolismInvolvement of genesIllumina MethylationEPICDNA methylationRelevant gene expressionEpigenetic modificationsExpression pairsInflammatory markersInflammatory responseLociHead and neck cancer patientsAssociated with inflammatory markersGenesDNAMarkers of inflammationAssociated with fatigueExpressionMethylationPost-radiotherapy
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